How to extract chloroplast genes from exon capture data using reference chloroplast genome

Question

[mdgn]

Hello everyone,

I have Megahit assemblies of 5 closely related plant species from targeted sequence capture (exons). What I want to do is, using a previously assembled reference chloroplast genome to extract the cp genes (exons) from these 5 assemblies to use them in maternal phylogeny. Sadly, my script writing capabilities are very limited. So I don't know how to continue from here.

I also use Geneious software to map the assemblies to the annotated reference, but i don't know if I can just "copy" mapped regions corresponding to genes from these assemblies.

I hope I explained my problem clear enough. Thanks in advance.